Project query data onto PCA reference

Source: R/project_query.R

Projects data from Seurat object onto a pre-computed PCA

project_query(
  new,
  reference,
  max.iter.harmony = 20,
  recompute_alignment = TRUE,
  seed = 66,
  ...
)

Arguments

new

A Seurat object containing cells to be projected
reference

A Seurat object after running getFeatureSpace()
max.iter.harmony

Maximum number of rounds to run Harmony. One round of Harmony involves one clustering and one correction step.
recompute_alignment

Recompute alignment? Useful if scPredict() has already been run
seed

Numeric seed for harmony
...

Further arguments to HarmonyMatrix()

Value

A Seurat object with two new reductions:

  • scpred: Aligned data using harmony

  • scpred_projection: Raw projection using reference loadings

Author

José Alquicira Hernández